Bank Reconciliation
You may reconcile other bank transactions using Workday native reconciliation functionality by creating a Matching Rule Set to define automated reconciliation rules. If you've been importing data with another method (a file-based import like FTP, for example) and the data is the same, your existing Matching Rules should continue to work as is.
You may also use the Manual Bank Reconciliation task:
Payment Reconciliation
Transactions that begin as Bank Connect payments will be available for reconciliation using the Payment Acknowledgements business process.